Knockdown of carbonate anhydrase elevates Nannochloropsis productivity at high CO2 level

Improving acid tolerance is pivotal to the development of microalgal feedstock for converting flue gas to biomass or oils. In the industrial oleaginous microalga Nannochloropsis oceanica, transcript knockdown of a cytosolic carbonic anhydrase (CA2), which is a key Carbon Concentrating Mechanism (CCM) component induced under 100 ppm CO2 (very low carbon, or VLC), results in ∼45%, ∼30% and ∼40% elevation of photosynthetic oxygen evolution rate, growth rate and biomass accumulation rate respectively under 5% CO2 (high carbon, or HC), as compared to the wild type. Such high-CO2-level activated biomass over-production is reproducible across photobioreactor types and cultivation scales. Transcriptomic, proteomic and physiological changes of the mutant under high CO2 (HC; 5% CO2) suggest a mechanism where the higher pH tolerance is coupled to reduced biophysical CCM, sustained pH hemostasis, stimulated energy intake and enhanced photosynthesis. Thus “inactivation of CCM” can generate hyper-CO2-assimilating and autonomously containable industrial microalgae for flue gas-based oil production. •In the industrial oleaginous microalga Nannochloropsis oceanica, a cytosolic carbonic anhydrase (CA2) was identified as a key Carbon Concentrating Mechanism (CCM) component induced in response to lowered CO2 level.•Knockdown of CA2 resulted in ~40% elevation of biomass accumulation rate under 5% CO2 (versus the wild type), which is reproducible across photobioreactor types and cultivation scales.•The higher pH tolerance of CA2-knockdown mutant is underpinned by reduced biophysical CCM, sustained pH hemostasis, stimulated energy intake and enhanced photosynthesis.•"Inactivation of CCM" is an effective strategy to generate hyper-CO2-assimilating and autonomously containable industrial microalgae for flue gas-based oil production.